Same observation in both FS9 and FSX. Without knowing how FS calculates acceleration vectors, I will not rely on those values while on ground where different forces apply (idle engine thrust, brake force, ground friction). Whatever it may be it seems fluctuations of body-axe longitudinal acceleration (3070) mainly depend on brake action (fixed small positive value when brakes are ON, small variations around 0 when brakes are released and aircraft is not moving). No more idea by now.

I can override output when aircraft is on ground and parking brake is set, that is not an issue.

But problem could be if I can't rely on this offset in flight. I am writing complex autopilot using PID controllers. I would like to use Z acceleration for IAS mode by pitch. This is chain of several controllers first PI setting required acceleration to get to proper IAS and second PID comparing this required acceleration against actual acceleration (this FSUIPC offset) and giving required pitch as its output.

Has anyone used this offset for such in-flight calculations?

There is still possibility to calculate Z acceleration as change in IAS over given time, which is coming to my mind more often now.

Tests I performed with AFSD indicate body-axe accelerations are ok while in flight. Most advanced aerodynamical calculations (CD,CL,etc) I perform are partly based on them and I didn't find any noticeable discrepancy. I also recalculate flight path-based accelerations from them without major problems. So you should have a try